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- PDB-1f1m: CRYSTAL STRUCTURE OF OUTER SURFACE PROTEIN C (OSPC) -

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Basic information

Entry
Database: PDB / ID: 1f1m
TitleCRYSTAL STRUCTURE OF OUTER SURFACE PROTEIN C (OSPC)
ComponentsOUTER SURFACE PROTEIN C
KeywordsIMMUNE SYSTEM / LYME DISEASE / OSPC / HB19 / HELICAL BUNDLE / DIMER
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
Lipoprotein, type 6 / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsKumaran, D. / Eswaramoorthy, S. / Dunn, J.J. / Swaminathan, S.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi.
Authors: Kumaran, D. / Eswaramoorthy, S. / Luft, B.J. / Koide, S. / Dunn, J.J. / Lawson, C.L. / Swaminathan, S.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER SURFACE PROTEIN C
B: OUTER SURFACE PROTEIN C
C: OUTER SURFACE PROTEIN C
D: OUTER SURFACE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,21410
Polymers70,8214
Non-polymers3926
Water11,385632
1
A: OUTER SURFACE PROTEIN C
B: OUTER SURFACE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6075
Polymers35,4112
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-104 kcal/mol
Surface area14530 Å2
MethodPISA
2
C: OUTER SURFACE PROTEIN C
D: OUTER SURFACE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6075
Polymers35,4112
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-104 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.323, 46.252, 111.784
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.59705, -0.32579, 0.73307), (-0.3256, -0.73675, -0.5926), (0.73316, -0.5925, 0.3338)28.16184, 6.58519, -12.53996
2given(0.97204, -0.04359, -0.23075), (0.04038, 0.99901, -0.0186), (0.23134, 0.00877, 0.97283)-7.59231, 46.31206, 63.02997

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Components

#1: Protein
OUTER SURFACE PROTEIN C / OSPC


Mass: 17705.262 Da / Num. of mol.: 4 / Fragment: RESIDUES 38-201 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: HB19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AGB1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 550, MES, Zinc sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.9 mg/mlprotein1drop
225 %(v/v)mPEG5501reservoir
310 mMzinc sulfate heptahydrate1reservoir
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Feb 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 53350 / % possible obs: 85.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.216 / % possible all: 21.6
Reflection
*PLUS
Num. obs: 531522

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Processing

Software
NameClassification
PHASESphasing
SHARPphasing
CNSrefinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→50 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2396 -RANDOM
Rwork0.201 ---
obs0.201 47286 75.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 6 632 5534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.01
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 48910 / Num. reflection Rfree: 2612 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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